Design and Synthesis of De Novo Peptide for Manganese Binding

The de novo peptide with 63-residues (MHB) has been synthesized biochemically and used for the binding of manganese (II) ions. In designed peptide, the leucine of the peptide dA1 (prototype) was replaced by His27 and Asp41 for binding the manganese (II) ions. The different chromatography studies and mass determination showed that new peptide folds into a monomeric, highly helical with a active site structure similar to the native Mn–SOD in an aqueous solution. Electron paramagnetic resonance (EPR) study suggested that the peptide binds single manganese (II) ion per molecule loosely with K _D value of about 36 μM. The circular dichroism (CD) studies demonstrated that the helical contents of the peptide did not change significantly even after binding the metal ions. The SOD activity study of the Mn–peptide complex showed that the IC₅₀ values is 8.08 μM.     

Copper sensing based on the far-red fluorescent protein, HcRed, from Heteractis crispa

In this article, we report for the first time on the copper (Cu(2+)) binding characteristics of the far-red fluorescent protein, HcRed, and its application in the development of a reagentless sensing system for copper. The far-red emission of HcRed (lambda(max) = 645 nm) where background cellular fluorescence is low should prove to be advantageous in the development of the sensing system. In the studies performed in our laboratory, we found that the fluorescence of HcRed is quenched in the presence of copper ions (Cu(2+)). The results obtained through UV-visible and circular dichroism spectra generated in the presence and absence of copper, as well as Stern-Volmer plots at different temperatures, indicate static quenching of HcRed fluorescence in the presence of copper, possibly through the formation of a copper-protein complex. On the basis of this observation, we developed a reagentless sensing system for the detection of copper(II) based on HcRed as the biosensing element. A detection limit for Cu(2+) in the nanomolar range was obtained. HcRed was found to bind copper ions selectively when compared with other divalent ions. A dissociation constant of 3.6muM was observed for copper binding. Histidine and cysteine residues are commonly involved in copper binding within proteins; therefore, to investigate the role of these amino acids present in HcRed, we chemically modified Cys and His residues using iodoacetamide and diethyl pyrocarbonate, respectively. The effect of copper addition on the fluorescence of the chemically modified HcRed was investigated. The His modification of HcRed substantially affected copper ion binding, pointing to histidine as the possible amino acid residue involved in the binding of copper ions in HcRed. A purification strategy for HcRed was also developed based on a copper immobilized affinity column without the addition of any affinity tag on the protein. The HcRed-based copper sensing system can potentially be employed to perform intracellular copper detection by genetically encoding the biosensing element or can be employed in environmental sensing.     

The Electrostatic Interactions Between Nano-TiO<Subscript>2</Subscript> and Trypsin Inhibit the Enzyme Activity and Change the Secondary Structure of Trypsin

In this work, the interaction between nano-TiO₂ and trypsin was investigated, and the mechanisms of the interaction were explored by the methods of UV–vis detection, circular dichroism (CD), and fluorescence. The results clearly demonstrated that nano-TiO₂ had an inhibitory effect on the enzyme activity. The activity was decreased to 64% of the untreated trypsin in the presence of 300 μg/ml nano-TiO₂. UV spectrometry proved that nano-TiO₂ had a strong physical absorption effect on trypsin, and the CD spectra revealed that the secondary structure of trypsin was partly destroyed while bound together with nano-TiO₂. The ratio of α-helix increased from 7.9% to 12.8% in the presence of 100 μg/ml TiO₂ while the ratio of β-sheet decreased from 48.7% to 36.4%. Furthermore, the fluorescence spectrometry indicated that nano-TiO₂ could quench the intrinsic fluorescence of trypsin through static quenching. Meanwhile, the binding constant was calculated to be 1, and the process of binding of trypsin on nano-TiO₂ was a spontaneous molecular interaction procedure in which electrostatic interaction plays a major role. Our study was to provide a useful approach for evaluating the health risk of nanomaterials on level of proteins.     

Co-expression of zinc binding motif and GFP as a cellular indicator of metal ions mobility

A significant role of zinc-binding motifs on metal mobility in Escherichia coli was explored using a chimeric metal-binding green fluorescent protein (GFP) as an intracellular zinc indicator. Investigation was initiated by co-transformation and co-expression of two chimeric genes encoding the chimeric GFP carrying hexahistidine (His6GFP) and the zinc-binding motif fused to outer membrane protein A (OmpA) in E. coli strain TG1. The presence of these two genes was confirmed by restriction endonucleases analysis. Co-expression of the two recombinant proteins exhibited cellular fluorescence activity and enhanced metal-binding capability of the engineered cells. Incorporation of the zinc-binding motif onto the membrane resulted in 60-fold more binding capability to zinc ions than those of the control cells. The high affinity to metal ions of the bacterial surface influenced influx of metal ions to the cells. This may affect the essential ions for triggering important cell metabolism. A declining of fluorescent intensity of GFP has been detected on the cell expressed of zinc binding motif. Meanwhile, balancing of metal homeostasis due to the presence of cytoplasmic chimeric His6GFP enhanced the fluorescent emission. These findings provide the first evidence of real-time monitoring of intracellular mobility of zinc by autofluorescent proteins.     

DNA damage in mouse lymphocytes exposed to curcumin and copper

Dietary polyphenolics, such as curcumin, have shown antioxidant and anti-inflammatory effects. Some antioxidants cause DNA strand breaks in excess of transition metal ions, such as copper. The aim of this study was to evaluate thein vitro effect of curcumin in the presence of increasing concentrations of copper to induce DNA damage in murine leukocytes by the comet assay. Balb-C mouse lymphocytes were exposed to 50 μM curcumin and various concentrations of copper (10 μM, 100 μM and 200 μM). Cellular DNA damage was detected by means of the alkaline comet assay. Our results show that 50 μM curcumin in the presence of 100–200 μM copper induced DNA damage in murine lymphocytes. Curcumin did not inhibit the oxidative DNA damage caused by 50 μM H₂O₂ in mouse lymphocytes. Moreover, 50 μM curcumin alone was capable of inducing DNA strand breaks under the tested conditions. The increased DNA damage by 50 μM curcumin was observed in the presence of various concentrations of copper, as detected by the alkaline comet assay.     

Trace metal concentrations in the tropical sponge Spheciospongia vagabunda at a sewage outfall: synchrotron X-ray imaging reveals the micron-scale distribution of accumulated metals

Major and trace elements were measured in sponges, seawater and sediment in Darwin Harbour (Australia) to test the hypothesis that metals are elevated in sponges closer to a sewage outfall compared with unimpacted sites. Seawater and sediment at the sewage discharge site contained high, but localised, concentrations of phosphorus (P), manganese (Mn), iron (Fe), cobalt (Co), nickel (Ni), copper (Cu), zinc (Zn), arsenic (As) and lead (Pb) compared with background sites. Metal concentrations in the sponge Spheciospongia vagabunda were highly elevated compared with other sponges and, although site specific, high metal concentrations were unrelated to the presence of sewage effluent. X-ray fluorescence microprobe imaging was used to investigate the metal distribution pattern in S. vagabunda. High Fe, Ni and Zn concentrations were either localised in circular patches (100–200 μm size) near water canals or in the pinacoderm, or scattered in spots (approximately 10 μm) throughout the tissue. This supports a microflora-mediated metal bioaccumulation hypothesis. In contrast, Co and Mn were highly dispersed and probably associated with aluminium- and iron-oxide rich sediment inclusions. Although the lack of association between sewage effluent and metal accumulation precludes the use of S. vagabunda as a biomonitor, the apparent differential mechanisms of metal accumulation warrants further investigation.     

Studies on the interaction between benzophenone and bovine serum albumin by spectroscopic methods

The interaction between benzophenone (BP) and bovine serum albumin (BSA) was investigated by the methods of fluorescence spectroscopy combined with UV–Vis absorption and circular dichroism (CD) measurements under simulative physiological conditions. The experiment results showed that the fluorescence quenching of BSA by BP was resulted from the formation of a BP–BSA complex and the corresponding association constants (K _a) between BP and BSA at four different temperatures had been determined using the modified Stern–Volmer equation. The enthalpy change (ΔH) and entropy change (ΔS) were calculated to be –43.73 kJ mol⁻¹ and −53.05 J mol⁻¹ K⁻¹, respectively, which suggested that hydrogen bond and van der Waals force played major roles in stabilizing the BP–BSA complex. Site marker competitive experiments indicated that the binding of BP to BSA primarily took place in site I (sub-domain IIA). The conformational investigation showed that the presence of BP decreased the α-helical content of BSA and induced the slight unfolding of the polypeptides of protein, which confirmed some micro-environmental and conformational changes of BSA molecules.     

Improved and high throughput quantitative measurements of weak GFP expression in transgenic plant materials

Green fluorescent proteins (GFPs) are widely used in tracing transgene expression and have been known as convenient and efficient markers for plant transformation. However, sometimes researchers are still puzzled by the weak fluorescence since it makes the observation of GFP signals and confirmation of transgenic plants difficult. In this investigation, we explored the possibility of enhancing the weak signals by changing the pH environment of detection and took microplate reader as a more effective instrument compared to traditional fluorescent microscope to detect the weak signals. It was found that the fluorescence intensity of enhanced GFP (EGFP) in transgenic plants can be increased 2–6 folds by altering the environmental pH, and the concentration of EGFP at a large scale (ranged from 20 ng/ml to 20 μg/ml) can be detected and quantified. It can exclude the influence of degradation fragment and hence facilitate later analysis; these advantages were further verified by comparing with western blotting and confocal microscopy. It was reliable and effective for the qualitative and quantitative analysis of transgenic plants and was more suitable for the detection of very weak fluorescent signals.     

Thermal aggregation and ion-induced cold-gelation of bovine serum albumin

Protein cold-gelation has recently received particular attention for its relevance in bio and food technology. In this work, we report a study on bovine serum albumin cold-gelation induced by copper or zinc ions. Metal-induced cold-gelation of proteins requires two steps: during the first one, the heat treatment causes protein partial unfolding and aggregation; then, after cooling the solution to room temperature, gels are formed upon the addition of metal ions. The thermally induced behaviour has been mainly investigated through different techniques: Fourier transform infrared (FTIR) spectroscopy, circular dichroism, dynamic light scattering (DLS) and rheology. Data have shown that the aggregation process is mainly due to protein conformational changes—α-helices into β-aggregates—forming small aggregated structures with a mean diameter of about 20 nm a few minutes after heating. After metal ion addition, the viscoelastic properties of the gels have been investigated by rheological measurements. The behaviour of the elastic and viscous moduli as a function of time is discussed in terms of ion concentration and type. Our results show that: (1) the elastic behaviour depends on ion concentration and (2) at a given ion concentration, gels obtained in the presence of zinc exhibit an elastic value larger than that observed in the Cu²⁺ case. Data suggest that cold-gelation is the result of different mechanisms: the ion-mediated protein–protein interaction and the bridging effect due to the presence of divalent ions in solution.     

A new Schiff base as a turn‐off fluorescent sensor for Cu2+ and its photophysical properties

A new Schiff base receptor 1 was synthesized and its photophysical properties were investigated by absorption, emission and excitation techniques. Furthermore, its chromogenic and fluorogenic sensing abilities towards various metal ions were examined. Receptor 1 selectively detects Cu²⁺ ion through fluorescence quenching and detection was not inhibited in the presence of other metal ions. From fluorescence titration, the limit of detection of receptor 1 as a fluorescent ‘turn‐off’ sensor for the analysis of Cu²⁺ was estimated to be 0.35 μM.     

Copper (II) complex of 1,10-phenanthroline and <Emphasis Type="SmallCaps">l</Emphasis>-tyrosine with DNA oxidative cleavage activity in the gallic acid

Copper (II) complex of formulation [Cu–Phen–Tyr](H₂O)](ClO₄) (Phen = 1,10-phenanthroline, l-Tyr = l-tyrosine), has been prepared, and their induced DNA oxidative cleavage activity studied. The complex binds to DNA by intercalation, as deduced from the absorption and fluorescence spectral data. Scatchard plots constructed from the absorption titration data gave binding constant 2.44 × 10⁴ M⁻¹ of base pairs. Extensive hypochromism, broadening, and red shifts in the absorption spectra were observed. Upon binding to DNA, the fluorescence from the DNA–ethidium bromide system was efficiently quenched by the copper (II) complex. Stern–Volmer quenching constant 0.61 × 10³ M⁻¹ obtained from the linear quenching plots. [Cu–Phen–Tyr] complex efficiently cleave the supercoiled DNA to its nicked circular form with gallic acid as biological reductant at appropriate complex concentration. The gallic acid as reductant could observably improve copper (II) complex to DNA damage. The pseudo-Michaelis–Menten kinetic parameters (k _cat, K _M) were calculated to be 1.32 h⁻¹ and 5.46 × 10⁻⁵ M for [Cu–Phen–Tyr] complex. Mechanistic studies reveal the involvement of superoxide anions and hydroxyl radical (HO^·) as the reactive species under an aerobic medium.     

Electronic and geometric structures of the organophosphate-degrading enzyme from <Emphasis Type="Italic">Agrobacterium radiobacter</Emphasis> (OpdA)

The organophosphate-degrading enzyme from Agrobacterium radiobacter (OpdA) is a highly efficient catalyst for the degradation of pesticides and some nerve agents such as sarin. OpdA requires two metal ions for catalytic activity, and hydrolysis is initiated by a nucleophilic hydroxide that is bound to one of these metal ions. The precise location of this nucleophile has been contentious, with both a terminal and a metal-ion-bridging hydroxide as likely candidates. Here, we employed magnetic circular dichroism to probe the electronic and geometric structures of the Co(II)-reconstituted dinuclear metal center in OpdA. In the resting state the metal ion in the more secluded α site is five-coordinate, whereas the Co(II) in the solvent-exposed β site is predominantly six-coordinate with two terminal water ligands. Addition of the slow substrate diethyl 4-methoxyphenyl phosphate does not affect the α site greatly but lowers the coordination number of the β site to five. A reduction in the exchange coupling constant indicates that substrate binding also triggers a shift of the μ-hydroxide into a pseudoterminal position in the coordination sphere of either the α or the β metal ion. Mechanistic implications of these observations are discussed.     

Equimolar Mixture of 2,2,2-Trifluoroethanol and 4-Chloro-1-butanol is a Stronger Inducer of Molten Globule State: Isothermal Titration Calorimetric and Spectroscopic Studies

A mixture of 4-chloro-1-butanol and 2,2,2-Trifluoroethanol (TFE) has been used to generate Molten globule (MG) state of structurally homologous but functionally different proteins bovine α-lactalbumin and hen egg-white lysozyme. The thermal denaturation was done using UV–Visible spectroscopy. From UV–Visible profile, thermal transition was not observed beyond a particular concentration. There was an indication of molten globule state in case of α-lactalbumin from circular dichroism experiments. By intrinsic tryptophan fluorescence, acrylamide and potassium iodide quenching, 8-anilino-naphthalene sulfonic acid (ANS) binding and energy transfer studies the presence of molten globule state was confirmed. Quantitative characterization of MG state and determining the binding thermodynamics of ANS to the MG state was done using Isothermal Titration Calorimetry (ITC). Results show that α-lactalbumin exists in MG state at a particular concentration but lysozyme does not show features of MG state.     

Preparation and Properties of Recombinant Rat and Human Procholecystokinin57 –95

Recombinant human progastrin_6–80 binds two ferric ions with an apparent dissociation constant of 2.2 ± 0.1 μM [Baldwin (2004) Protein J 23:65–70]. The aims of the present study were to express fragments of recombinant procholecystokinin and to determine whether or not they bound ferric ions. Recombinant rat and human procholecystokinin_57–95 were expressed as glutathione S-transferase fusion proteins in E. coli. The fusion proteins were bound to glutathione-agarose, cleaved with thrombin, and purified by reverse phase HPLC. Recombinant procholecystokinin_57–95 did not bind to either the CCK1 or CCK2 receptor with high affinity. No change in absorption spectrum was observed on addition of ferric ions, and analysis of the quenching of tryptophan fluorescence observed in the presence of ferric ions indicated that binding to procholecystokinin_57–95 was at least 40–fold weaker than the binding of ferric ions to progastrin_6–80.     

Anchorage of GFP fusion on the cell surface of <Emphasis Type="Italic">Pseudomonas putida</Emphasis>

Here we report the cell surface display of organophosphorus hydrolase (OPH) and green fluorescent protein (GFP) fusion by employing the N- and C-terminal domains of ice nucleation protein (INPNC) as an anchoring motif. An E. coli–Pseudomonas shuttle vector, pNOG33, coding for INPNC–OPH–GFP was constructed for targeting the fusion onto the cell surface of p-nitrophenol (PNP)-degrading P. putida JS444. The surface localization of INPNC–OPH–GFP was verified by cell fractionation, Western blot, proteinase accessibility, and immunofluorescence microscopy. Furthermore, the functionality of the surface-exposed OPH–GFP was demonstrated by OPH assays and fluorescence measurements. Surface display of macromolecular OPH–GFP fusion (63 kDa) neither inhibited cell growth nor affected cell viability. These results suggest that INP is an useful tool for the presentation of heterologous proteins on cell surfaces of indigenous microbes. The engineered P. putida JS444 degraded organophosphates (OPs) as well as PNP rapidly and could be easily monitored by fluorescence. Parathion (100 mg kg⁻¹) could be degraded completely within 15 days in soil inoculated with the engineered strain. These merits make this engineered strain an ideal biocatalyst for in situ bioremediation of OP-contaminated soil.     

Copper complexing properties of dissolved organic matter: PARAFAC treatment of fluorescence quenching

Fluorescence quenching of the fluorescence is a useful method to determine copper complexing properties of the dissolved organic matter. This technique provides express results often by choosing one or two excitation-emission fluorescence measurement for a straight range of concentration. That why it is not representative of the whole sample. On another hand, using total luminescence spectra gives lots of information that is difficult to manipulate in term of complexing properties. This work focus on a fluorescence quenching experiment carried out on a filtered black water from Rio Negro from north Brazil (Sao Gabriel da Cachoeira) using excitation emission matrix of fluorescence (EEMF) with a large range of copper concentration. Indeed, metal additions were performed using logarithmic increments of the total copper concentration to cover a wide range of concentration from 1.7 × 10⁻⁹ to 10⁻³ mol l⁻¹. These data were treated by two different ways for comparison: on the one hand, data treatment were computed, as usually, at different fluorescence intensity positions using multi-response wavelength method with two ligand, and, on the another hand, a statistical method, parallel factor analysis (PARAFAC), was applied to extract fluorescent component. Then a fitting was done on these PARAFAC components with one or two complexing sites each one. Results show that PARAFAC enables quantitative evaluation of complexing parameters for copper as good as certain multi-response methods: L_1T 16.2 × 10⁻⁶ mol l⁻¹ (5.0 < log(K₁) < 5.8) and L_2T 3.0 × 10⁻⁴ mol l⁻¹ (2.8 < log(K₂) < 3.9). PARAFAC confirms that for this natural sample only two fluorescent ligands are present with two types of site for each component. No residual fluorescence was detected by the statistical treatment. Wall surface interferences were pointed-out as phenomenon to be solve to overcome the limiting efficiency of the total copper concentration range.     

Al (III) metal augment thermal aggregation and fibrillation in protein: Role of metal toxicity in neurological diseases

Protein fibrillation is a leading cause of innumerable neurodegenerative diseases. The exact underlying mechanism associated with the formation of fibrils is yet to be known. Recently, the role of metal ions resulting into fibrillation of proteins has gained attention of the scientific community. In this piece of work, we have investigated the effect of the aluminum (Al) metal ion on the kinetics of aggregation of bovine serum albumin (BSA) protein under physiological conditions by employing several biophysical and microscopic techniques. Quenching of tryptophan fluorescence was observed along with 9 nm blue shift, demonstrating BSA becomes more hydrophobic during unfolding pathway of thermal denaturation. Moreover, ANS (8-Anilino-1-naphthalene sulfonic acid) binding shows quenching in fluorescence intensity with increasing time of incubation at 65 °C, suggesting unfolding leading to the disruption of hydrophobic patches in BSA. Besides, Thioflavin T intensity indicated a significant acceleration in BSA fibrillation at a ratio of 1:1 and 1:2 of BSA and Al (III) metal ion respectively. In addition, circular dichroism (CD) spectroscopy study revealed the transition of BSA from α-helical conformation to the β-sheet rich structure. Molecular docking analysis demonstrated significant binding affinity (−1.2 kcal/mol) of Al (III) with BSA involving Phe501, Phe506, Val575, Thr578, Gln579, Leu531 residues. Transmission electron microscopy (TEM) reaffirm augmentation of thermal-induced BSA fibril formation in the presence of Al (III) metal ions. This study highlights the metal chelating potency as the possible therapeutic target for neurological diseases.     

Recombination of the GFP gene to the BFP gene using a man-made site-selective DNA cutter

By using the recently developed man-made DNA cutter [a combination of Ce(IV)/EDTA and two DNA additives], green fluorescent protein (GFP) was converted to closely related blue fluorescent protein (BFP). The phosphodiester linkages at T196-A200 in the sense strand of GFP were hydrolyzed by the cutter, and the A1-T196 fragment in the product was selectively connected with the downstream fragment (C197-A720) of BFP by T4 DNA ligase. This recombination changed three codons in the GFP gene (TGC at 196–198, TAT at 199–201, and ACC at 502–504) to TCT, CAT, and ATC in BFP, and accordingly three amino acids in GFP (Cys65, Tyr66, and Thr167) were altered to Ser65, His66, and Ile167. The recombinant gene was successfully expressed in Escherichia coli and emitted blue fluorescence, confirming the absence of undesired side reactions (mutation, deletion, insertion, depurination, etc.) in the DNA manipulation. Electronic Supplementary Material Supplementary material is available for this article at and is accessible for authorized users.     

Influence of copper(II) and magnesium(II) ions on the ciprofloxacin binding to DNA

The influence of magnesium(II) and copper(II) ions on the binding of ciprofloxacin to double stranded calf thymus DNA was studied by fluorescence emission spectroscopy, ultraviolet- and circular dichroism (CD) spectroscopy. The interaction of ciprofloxacin and copper(II) ions was followed by strong fluorescence quenching which was almost unaffected by the presence of DNA. On the other hand, only a slight decrease in fluorescence emission intensity, which was enhanced in the presence of DNA, was observed for ciprofloxacin interaction with magnesium(II) ions. Furthermore, magnesium(II) ions increase the thermal stability of the DNA, while, in the presence of ciprofloxacin, the degree of stabilisation is smaller. In contrast, copper(II) ions destabilise double helical DNA to heat, while ciprofloxacin slightly affects only the second transition of the biphasic melting curve of calf thymus DNA. Magnesium(II) ions at 25 degrees C induce conformational transitions of DNA at concentrations of 1.5 mM and 2.5 M, as monitored by CD. On the other hand copper(II) ions induce only one conformational transition, at a concentration of 12.7 microM. At higher concentrations of copper(II) ions (c>700 microM) DNA starts to precipitate. Significant changes in the CD spectra of DNA were observed after addition of ciprofloxacin to a solution containing DNA and copper(II) ions, but not to DNA and magnesium(II) ions. Based on our spectroscopic results, we propose that copper(II) ions are not directly involved into ciprofloxacin binding to DNA via phosphate groups as it has been suggested for magnesium(II) ions.     

Metal ion accessibility of histidine-modified superfolder green fluorescent protein expressed in Escherichia coli

Green fluorescent protein (GFP) is frequently utilized for metal ion detection and quantification. To improve the metal binding potential of GFP, three residues (N146, F165, and L201) were substituted to histidines. Each variant responded differently upon interaction with metal ions. More than 80% of N146H, having the most accessible surface area, could bind to immobilized metal ions. However, only F165H exhibited significant differences in quenching by soluble metal ions (22% fluorescence decrease) in comparison with the template protein (12%). These findings can be utilized for designing GFP variants for metal binding and sensor applications.